mpa.ProfileInfo

Overview

profile_info is a program within the mpathic package which calculates the mutual information between base identity at a given position and expression for each position in the given data set.

Usage

>>> import mpathic as mpa
>>> mpa.ProfileInfo(dataset_df = dataset_df)

Example Input and Output

The input to the function must be a sorted library a column for sequences and columns of counts for each bin. For selection experiments, ct_0 should label the pre-selection library and ct_1 should be the post selection library. For MPRA experiments, ct_0 should label the sequence library counts, and ct_1 should label the mRNA counts.

Example input table:

seq       ct_0    ct_1     ct_2...
ACATT     1       4        3
GGATT     2       5        5
...

Example output table:

pos    info    info_err
0      .02     .004
1      .04     .004
...

The mutual information is given in bits.

Class Details

class profile_info.ProfileInfo(**kwargs)

Profile Info computes the mutual information (in bits), at each position, between the character and the bin number.

Parameters:

dataset_df: (pandas dataframe)

Input data frame

err: (boolean)

If true, include error estimates in computed mutual information

method: (string)

method used in computation. Valid choices inlcude: ‘naive’,’tpm’,’nsb’.

pseudocount: (float)

pseudocount used to compute information values

start: (int)

An integer specifying the sequence start position

end: (int)

An integer specifying the sequence end position

Returns:

info_df: (pandas dataframe)

dataframe containing results.